If the Social Security Number (SSN) on a Form W-2 is different from the Individual Taxpayer Identification Number (ITIN) number used to file the return, the wages are reported as being earned by the ITIN holder, and are taxable to the ITIN holder.  

Entering the correct SSN on the W-2 will make it easier for IRS systems to associate the wages with the ITIN holder. This will stop the IRS from sending a notice to the person whose SSN is being used and eliminates the need for that person to prove that they did not earn the wages. 

Per the IRS website: Individual Taxpayer Identification Number (ITIN) Reminders for Tax Professionals

Tax returns filed with an Individual Taxpayer Identification Number reporting wages paid are required to show the Social Security Number under which the wages were earned. This creates an identification number (ITIN/SSN) mismatch. In the past, returns with this mismatch could only be filed on paper. Due to programming changes the IRS' e-file system can now accept these returns.

The taxpayer's correct ITIN should be used as the identifying number at the top of Form 1040. When inputting W-2 information, the SSN should be entered exactly as shown on the Form W-2 issued by the employer. It is now possible to e-file a return with an ITIN/SSN mismatch.

In TaxAct, only the Professional version of the software allows overriding the ITIN number on the W-2 form (which was automatically transferred from the Basic Info section of the program), and replacing it with the Social Security Number that actually appears on the W-2 and still have the ability to electronically file the return. 

Desktop users of the program (who are not using the Professional version of the software) are able to override the number on the W-2, but must paper file the return as overridden fields are not allowed when electronically filing those returns.